contributing to open science
ISEM, 30 November 2023
People used to think that it was ok not to disclose every step of our work, including data and code
An advantage
A published article is just the tip of the iceberg that is the research process…
“An article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code and data, that produced the result.”
Claerbout and Karrenbach 1992.
Wilson et al. 2016. Plos Comp Biol. https://arxiv.org/pdf/1609.00037.pdf
1. Project Organization : File organisation
2. Data management
3. Software : Code structure & analysis flow
4. Tracking Changes : version management
5. Manuscripts
“Organizing the digital artifacts of a project to ease discovery and understanding.”
= Research compendium
Writing, organizing, and sharing scripts and programs used in an analysis.
Respect code conventions from your community, https://style.tidyverse.org/
Document your code
Document the workflow (what is done in what order with what)
Document software used (OS, versions of R, versions of functions)
Track the evolution of your project
Use a version control software (Git).
Writing manuscripts in a way that leaves an audit trail and minimizes manual merging of conflict.
LaTeX (e.g. overleaf)
Markdown
Quarto (https://quarto.org)
data
code
documentation (e.g. article)
Reproducible research